From 79b1ebe44b09ef8a896c6c42ce44798c26be1e53 Mon Sep 17 00:00:00 2001
From: Jean-Baptiste Keck <Jean-Baptiste.Keck@imag.fr>
Date: Wed, 4 Nov 2020 13:32:21 +0100
Subject: [PATCH] fix min max mpi reduction bug
---
ci/docker_images/ubuntu/groovy/Dockerfile | 6 +-
ci/scripts/test.sh | 55 +++---
.../backend/host/fortran/operator/poisson.py | 5 +
.../host/fortran/operator/scales_advection.py | 10 ++
hysop/backend/host/host_operator.py | 19 +-
hysop/core/graph/computational_graph.py | 10 +-
.../core/graph/computational_node_frontend.py | 5 +-
hysop/core/graph/continuous.py | 16 +-
hysop/core/tests/test_checkpoint.sh | 168 +++++++++---------
hysop/fields/tests/test_cartesian.sh | 2 +-
hysop/operator/adapt_timestep.py | 58 +++---
hysop/operator/advection.py | 2 +-
hysop/operator/base/external_force.py | 2 +
hysop/operator/base/memory_reordering.py | 6 +-
hysop/operator/base/min_max.py | 23 ++-
hysop/operator/directional/directional.py | 7 +-
hysop/operator/hdf_io.py | 6 +-
hysop/operator/mean_field.py | 4 +-
hysop/operator/misc.py | 2 +-
hysop/operator/parameter_plotter.py | 6 +-
.../operator/tests/test_bilevel_advection.py | 6 +-
hysop/operator/tests/test_scales_advection.py | 6 +-
hysop/tools/debug_dumper.py | 23 +--
hysop/tools/handle.py | 25 ++-
hysop_examples/argparser.py | 2 +-
.../examples/cylinder/oscillating_cylinder.py | 4 +-
.../flow_around_sphere/flow_around_sphere.py | 2 +-
.../particles_above_salt_bc.py | 4 +-
.../particles_above_salt_bc_3d.py | 4 +-
.../particles_above_salt_symmetrized.py | 4 +-
.../turbulent_scalar_advection.py | 2 +-
.../sediment_deposit/sediment_deposit.py | 4 +-
.../sediment_deposit_levelset.py | 4 +-
.../examples/taylor_green/taylor_green.py | 5 +-
.../taylor_green/taylor_green_cpuFortran.py | 2 +-
35 files changed, 282 insertions(+), 227 deletions(-)
diff --git a/ci/docker_images/ubuntu/groovy/Dockerfile b/ci/docker_images/ubuntu/groovy/Dockerfile
index 20099148b..8f4cc1513 100644
--- a/ci/docker_images/ubuntu/groovy/Dockerfile
+++ b/ci/docker_images/ubuntu/groovy/Dockerfile
@@ -50,9 +50,9 @@ RUN cd /tmp && \
cd /tmp && \
rm -Rf /tmp/hptt
-# HDF5 + h5py (v1.10.6 is currently the last supported by h5py)
+# HDF5 1.12.0 + h5py 3.0.0
RUN cd /tmp && \
- wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.6/src/hdf5-1.10.6.tar.gz && \
+ wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0.tar.gz && \
tar -xvzf hdf5-*.tar.gz && \
rm -f hdf5-*.tar.gz && \
cd hdf5-* && \
@@ -60,7 +60,7 @@ RUN cd /tmp && \
make && \
make install && \
rm -rf /tmp/hdf5-*
-RUN CC="${MPICC}" HDF5_MPI="ON" HDF5_VERSION="1.10.6" HDF5_DIR="${MPI_ROOT}" pip3.8 install --upgrade --no-binary=h5py h5py
+RUN CC="${MPICC}" HDF5_MPI="ON" HDF5_VERSION="1.12.0" HDF5_DIR="${MPI_ROOT}" pip3.8 install --upgrade --no-binary=h5py h5py
# other python packages (standard primefac package does not support python3)
RUN pip3.8 install --upgrade scipy sympy matplotlib gmpy2 psutil py-cpuinfo Mako editdistance portalocker colors.py tee pycairo argparse_color_formatter networkx pyvis zarr numcodecs jsonpickle memory-tempfile
diff --git a/ci/scripts/test.sh b/ci/scripts/test.sh
index 19c9a1029..7bd8ca02f 100755
--- a/ci/scripts/test.sh
+++ b/ci/scripts/test.sh
@@ -78,7 +78,8 @@ export PYOPENCL_COMPILER_OUTPUT=0
# OpenMPI specific variables
export OMPI_ALLOW_RUN_AS_ROOT=1
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
-export OMPI_MCA_rmaps_base_oversubscribe=1
+export OMPI_MCA_rmaps_base_oversubscribe=1
+export OMPI_MCA_btl_vader_single_copy_mechanism=none # see https://github.com/open-mpi/ompi/issues/4948
echo "Trying to load hysop module:"
${PYTHON_EXECUTABLE} -c 'import hysop; print(hysop)'
@@ -93,9 +94,9 @@ RUN_EXAMPLES=${RUN_EXAMPLES:-true}
RUN_LONG_TESTS=${RUN_LONG_TESTS:-false}
COMMON_TEST_OPTIONS=''
-TEST_DIR="$HYSOP_DIR"
+TEST_DIR="${HYSOP_DIR}"
COMMON_EXAMPLE_OPTIONS='-VNC -d16 -cp float -maxit 2 --autotuner-max-candidates 1 --save-checkpoint --checkpoint-dump-freq 0 --checkpoint-dump-period 0 --checkpoint-dump-last --checkpoint-dump-times'
-EXAMPLE_DIR="$HYSOP_DIR/../hysop_examples/examples"
+EXAMPLE_DIR="${HYSOP_DIR}/../hysop_examples/examples"
hysop_test() {
test=$1
@@ -115,29 +116,31 @@ example_test() {
}
if [ "$RUN_TESTS" = true ]; then
- hysop_test "core/arrays/tests/test_array.py"
- hysop_test "core/graph/tests/test_graph.py"
- hysop_test "fields/tests/test_fields.py"
- hysop_test "numerics/tests/test_fft.py"
- hysop_test "operator/tests/test_analytic.py"
- hysop_test "operator/tests/test_transpose.py"
- hysop_test "operator/tests/test_fd_derivative.py"
- hysop_test "operator/tests/test_absorption.py"
- hysop_test "operator/tests/test_penalization.py"
- hysop_test "operator/tests/test_velocity_correction.py"
- hysop_test "operator/tests/test_restriction_filter.py"
- hysop_test "operator/tests/test_directional_advection.py"
- hysop_test "operator/tests/test_directional_diffusion.py"
- hysop_test "operator/tests/test_directional_stretching.py"
- hysop_test "operator/tests/test_custom_symbolic.py"
- hysop_test "operator/tests/test_spectral_derivative.py"
- hysop_test "operator/tests/test_spectral_curl.py"
- hysop_test "operator/tests/test_diffusion.py"
- hysop_test "operator/tests/test_poisson.py"
- hysop_test "operator/tests/test_solenoidal_projection.py"
- hysop_test "operator/tests/test_poisson_curl.py"
- ${HYSOP_DIR}/fields/tests/test_cartesian.sh
- #${HYSOP_DIR}/core/tests/test_checkpoint.sh
+ #hysop_test "core/arrays/tests/test_array.py"
+ #hysop_test "core/graph/tests/test_graph.py"
+ #hysop_test "fields/tests/test_fields.py"
+ #hysop_test "numerics/tests/test_fft.py"
+ #hysop_test "operator/tests/test_analytic.py"
+ #hysop_test "operator/tests/test_transpose.py"
+ #hysop_test "operator/tests/test_fd_derivative.py"
+ #hysop_test "operator/tests/test_absorption.py"
+ #hysop_test "operator/tests/test_penalization.py"
+ #hysop_test "operator/tests/test_velocity_correction.py"
+ #hysop_test "operator/tests/test_restriction_filter.py"
+ #hysop_test "operator/tests/test_scales_advection.py"
+ #hysop_test "operator/tests/test_bilevel_advection.py"
+ #hysop_test "operator/tests/test_directional_advection.py"
+ #hysop_test "operator/tests/test_directional_diffusion.py"
+ #hysop_test "operator/tests/test_directional_stretching.py"
+ #hysop_test "operator/tests/test_custom_symbolic.py"
+ #hysop_test "operator/tests/test_spectral_derivative.py"
+ #hysop_test "operator/tests/test_spectral_curl.py"
+ #hysop_test "operator/tests/test_diffusion.py"
+ #hysop_test "operator/tests/test_poisson.py"
+ #hysop_test "operator/tests/test_solenoidal_projection.py"
+ #hysop_test "operator/tests/test_poisson_curl.py"
+ #${HYSOP_DIR}/fields/tests/test_cartesian.sh
+ ${HYSOP_DIR}/core/tests/test_checkpoint.sh
fi
if [ "${RUN_LONG_TESTS}" = true ]; then
diff --git a/hysop/backend/host/fortran/operator/poisson.py b/hysop/backend/host/fortran/operator/poisson.py
index 6f5638ff9..c44b8608b 100644
--- a/hysop/backend/host/fortran/operator/poisson.py
+++ b/hysop/backend/host/fortran/operator/poisson.py
@@ -9,6 +9,11 @@ from hysop.constants import HYSOP_REAL
class PoissonFFTW(FortranFFTWOperator):
+ def __new__(cls, Fin, Fout, variables,
+ extra_input_kwds=None, **kwds):
+ return super(PoissonFFTW, cls).__new__(cls,
+ input_fields=None, output_fields=None, **kwds)
+
def __init__(self, Fin, Fout, variables,
extra_input_kwds=None, **kwds):
"""Operator to solve Poisson equation using FFTW in Fortran.
diff --git a/hysop/backend/host/fortran/operator/scales_advection.py b/hysop/backend/host/fortran/operator/scales_advection.py
index 6d9206b67..1b930d04e 100644
--- a/hysop/backend/host/fortran/operator/scales_advection.py
+++ b/hysop/backend/host/fortran/operator/scales_advection.py
@@ -78,6 +78,16 @@ class ScalesAdvection(FortranOperator):
am.update(cls.__available_methods)
return am
+ @debug
+ def __new__(cls, velocity,
+ advected_fields_in, advected_fields_out,
+ variables, dt, **kwds):
+ return super(ScalesAdvection, cls).__new__(cls,
+ input_fields=None, output_fields=None,
+ input_params=None, output_params=None,
+ **kwds)
+
+
@debug
def __init__(self, velocity,
advected_fields_in, advected_fields_out,
diff --git a/hysop/backend/host/host_operator.py b/hysop/backend/host/host_operator.py
index b2bbf16ae..368cb9c3e 100644
--- a/hysop/backend/host/host_operator.py
+++ b/hysop/backend/host/host_operator.py
@@ -14,25 +14,32 @@ from hysop.core.graph.computational_operator import ComputationalGraphOperator
from hysop.topology.topology_descriptor import TopologyDescriptor
-class HostOperator(ComputationalGraphOperator, metaclass=ABCMeta):
+class HostOperatorBase(ComputationalGraphOperator, metaclass=ABCMeta):
"""
- Abstract class for discrete operators working on OpenCL backends.
+ Abstract class for discrete operators working on cpu.
+ HostOperatorBase ignore the extra cl_env keyword parameter.
"""
@debug
- def __new__(cls, **kwds):
- return super(HostOperator, cls).__new__(cls, **kwds)
+ def __new__(cls, cl_env=None, **kwds):
+ return super(HostOperatorBase, cls).__new__(cls, **kwds)
@debug
- def __init__(self, **kwds):
+ def __init__(self, cl_env=None, **kwds):
"""
Create the common attributes of all host operators.
All input and output variable topologies should be of kind
Backend.HOST and share the same HostEnvironment.
"""
- super(HostOperator, self).__init__(**kwds)
+ super(HostOperatorBase, self).__init__(**kwds)
+
+class HostOperator(ComputationalGraphOperator, metaclass=ABCMeta):
+ """
+ Abstract class for discrete operators working on cpu.
+ HostOperator extra cl_env keyword parameter and enforces HOST backend.
+ """
@classmethod
def supported_backends(cls):
"""
diff --git a/hysop/core/graph/computational_graph.py b/hysop/core/graph/computational_graph.py
index 5535f39c6..e20bc9402 100644
--- a/hysop/core/graph/computational_graph.py
+++ b/hysop/core/graph/computational_graph.py
@@ -195,7 +195,7 @@ class ComputationalGraph(ComputationalGraphNode, metaclass=ABCMeta):
ss = '>INPUTS:'
if sinputs:
- for (td, sreqs) in sinputs.items():
+ for (td, sreqs) in sorted(sinputs.items()):
if isinstance(td, Topology):
ss += '\n {}'.format(td.short_description())
else:
@@ -205,7 +205,7 @@ class ComputationalGraph(ComputationalGraphNode, metaclass=ABCMeta):
discr_size=discr_size, ghosts_size=ghosts_size,
order_size=order_size, cansplit_size=cansplit_size,
tstates_size=tstates_size)
- for (opname, fname, discr, ghosts, order, can_split, tstates) in sreqs:
+ for (opname, fname, discr, ghosts, order, can_split, tstates) in sorted(sreqs):
ss += template.format(
opname, fname, discr, ghosts, order, can_split, tstates,
name_size=name_size, field_size=field_size,
@@ -216,7 +216,7 @@ class ComputationalGraph(ComputationalGraphNode, metaclass=ABCMeta):
ss += ' None'
ss += '\n>OUTPUTS:'
if soutputs:
- for (td, sreqs) in soutputs.items():
+ for (td, sreqs) in sorted(soutputs.items()):
if isinstance(td, Topology):
ss += '\n {}'.format(td.short_description())
else:
@@ -226,7 +226,7 @@ class ComputationalGraph(ComputationalGraphNode, metaclass=ABCMeta):
discr_size=discr_size, ghosts_size=ghosts_size,
order_size=order_size, cansplit_size=cansplit_size,
tstates_size=tstates_size)
- for (opname, fname, discr, ghosts, order, can_split, tstates) in sreqs:
+ for (opname, fname, discr, ghosts, order, can_split, tstates) in sorted(sreqs):
ss += template.format(
opname, fname, discr, ghosts, order, can_split, tstates,
name_size=name_size, field_size=field_size,
@@ -716,7 +716,7 @@ class ComputationalGraph(ComputationalGraphNode, metaclass=ABCMeta):
net = self.to_pyvis()
import tempfile
- with tempfile.NamedTemporaryFile(suffix='.html') as f:
+ with tempfile.NamedTemporaryFile(suffix='.html', delete=False) as f:
net.show(f.name)
def to_html(self, path, io_rank=0, show_buttons=False):
diff --git a/hysop/core/graph/computational_node_frontend.py b/hysop/core/graph/computational_node_frontend.py
index 35d830954..4595a5348 100644
--- a/hysop/core/graph/computational_node_frontend.py
+++ b/hysop/core/graph/computational_node_frontend.py
@@ -122,10 +122,11 @@ class ComputationalGraphNodeFrontend(ComputationalGraphNodeGenerator):
sargs = ['*{} = {}'.format(k,v.__class__)
for (k,v) in self.impl_kwds.items()]
msg = 'FATAL ERROR during {}.generate():\n'
- msg += ' => failed to call {}.__init__()\n with the following keywords:'
+ msg += ' => failed to initialize an instance of type {}'
+ msg += '\n by using the following keyword arguments:'
msg += '\n '+'\n '.join(sargs)
msg = msg.format(self.__class__, self.impl)
- print('\n{}\n'.format(msg))
+ print('\n{}'.format(msg))
raise
for kwds in self._input_fields_to_dump:
diff --git a/hysop/core/graph/continuous.py b/hysop/core/graph/continuous.py
index e5e545d54..5374fd349 100755
--- a/hysop/core/graph/continuous.py
+++ b/hysop/core/graph/continuous.py
@@ -25,13 +25,7 @@ class OperatorBase(TaggedObject, metaclass=ABCMeta):
@debug
def __new__(cls, name, fields, tensor_fields, parameters,
mpi_params=None, io_params=False, **kwds):
- try:
- return super(OperatorBase, cls).__new__(cls, tagged_cls=OperatorBase, tag_prefix='node', **kwds)
- except TypeError:
- if ('cl_env' not in kwds):
- raise
- kwds.pop('cl_env')
- return super(OperatorBase, cls).__new__(cls, tagged_cls=OperatorBase, tag_prefix='node', **kwds)
+ return super(OperatorBase, cls).__new__(cls, tagged_cls=OperatorBase, tag_prefix='node', **kwds)
@debug
def __init__(self, name, fields, tensor_fields, parameters, mpi_params=None, io_params=False, **kwds):
@@ -61,13 +55,7 @@ class OperatorBase(TaggedObject, metaclass=ABCMeta):
mpi_params: MPIParams
File i/o config (filename, format ...)
"""
- try:
- super(OperatorBase,self).__init__(tagged_cls=OperatorBase, tag_prefix='node', **kwds)
- except TypeError:
- if ('cl_env' not in kwds):
- raise
- kwds.pop('cl_env')
- super(OperatorBase,self).__init__(tagged_cls=OperatorBase, tag_prefix='node', **kwds)
+ super(OperatorBase,self).__init__(tagged_cls=OperatorBase, tag_prefix='node', **kwds)
check_instance(fields, tuple, values=ScalarField)
check_instance(tensor_fields, tuple, values=TensorField)
diff --git a/hysop/core/tests/test_checkpoint.sh b/hysop/core/tests/test_checkpoint.sh
index e64700965..f748ad47c 100755
--- a/hysop/core/tests/test_checkpoint.sh
+++ b/hysop/core/tests/test_checkpoint.sh
@@ -1,7 +1,8 @@
#!/usr/bin/env bash
set -feu -o pipefail
+set -x
PYTHON_EXECUTABLE=${PYTHON_EXECUTABLE:-python3.8}
-MPIRUN_EXECUTABLE=${MPIRUN_EXECUTABLE:-mpirun --allow-run-as-root}
+MPIRUN_EXECUTABLE=${MPIRUN_EXECUTABLE:-mpirun}
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
EXAMPLE_DIR="$(realpath ${SCRIPT_DIR}/../../../hysop_examples/examples)"
@@ -30,94 +31,93 @@ function compare_files {
#
# Basic test with 2D diffusion (serial)
#
-EXAMPLE_FILE="${EXAMPLE_DIR}/scalar_diffusion/scalar_diffusion.py"
-TEST_DIR='/tmp/hysop_tests/checkpoints/scalar_diffusion'
-COMMON_OPTIONS="-NC -impl opencl -cp fp32 -d64 --debug-dump-target dump -nu 0.02 -niter 20 -te 0.1 --dump-tstart 0.05 --dump-freq 1 "
-
-echo
-echo "TEST SCALAR DIFFUSION CHECKPOINT (SERIAL)"
-if [[ ! -f "${EXAMPLE_FILE}" ]]; then
- echo "Cannot find example file '${EXAMPLE_FILE}'."
- exit 1
-fi
-
-echo ' Running simulations...'
-"${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -S "${TEST_DIR}/checkpoint0.tar" --dump-dir "${TEST_DIR}/run0" --checkpoint-dump-time 0.05 --checkpoint-dump-freq 0
-"${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -S "${TEST_DIR}/checkpoint1.tar" --dump-dir "${TEST_DIR}/run1" --checkpoint-dump-time 0.05 --checkpoint-dump-freq 0
-
-echo ' Comparing solutions...'
-echo " >debug dumps match"
-compare_files "${TEST_DIR}/run0/dump/run.txt" "${TEST_DIR}/run1/dump/run.txt"
-for f0 in $(find "${TEST_DIR}/run0" -name '*.h5' | sort -n); do
- f1=$(echo "${f0}" | sed 's/run0/run1/')
- compare_files "${f0}" "${f1}"
- echo " >$(basename ${f0}) match"
-done
-
-echo
-echo ' Running simulations from checkpoints...'
-"${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -L "${TEST_DIR}/checkpoint0.tar" --dump-dir "${TEST_DIR}/run2"
-"${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -L "${TEST_DIR}/checkpoint1.tar" --dump-dir "${TEST_DIR}/run3"
-
-echo ' Comparing solutions...'
-compare_files "${TEST_DIR}/run2/dump/run.txt" "${TEST_DIR}/run3/dump/run.txt"
-echo " >debug dumps match"
-for f0 in $(find "${TEST_DIR}/run2" -name '*.h5' | sort -n); do
- f1=$(echo "${f0}" | sed 's/run2/run3/')
- f2=$(echo "${f0}" | sed 's/run2/run0/')
- f3=$(echo "${f0}" | sed 's/run2/run1/')
- compare_files "${f0}" "${f1}"
- compare_files "${f0}" "${f2}"
- compare_files "${f0}" "${f3}"
- echo " >$(basename ${f0}) match"
-done
+#EXAMPLE_FILE="${EXAMPLE_DIR}/scalar_diffusion/scalar_diffusion.py"
+#TEST_DIR='/tmp/hysop_tests/checkpoints/scalar_diffusion'
+#COMMON_OPTIONS="-NC -impl opencl -cp fp32 -d64 --debug-dump-target dump -nu 0.02 -niter 20 -te 0.1 --dump-tstart 0.05 --dump-freq 1 "
+
+#echo
+#echo "TEST SCALAR DIFFUSION CHECKPOINT (SERIAL)"
+#if [[ ! -f "${EXAMPLE_FILE}" ]]; then
+ #echo "Cannot find example file '${EXAMPLE_FILE}'."
+ #exit 1
+#fi
+
+#echo ' Running simulations...'
+#"${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -S "${TEST_DIR}/checkpoint0.tar" --dump-dir "${TEST_DIR}/run0" --checkpoint-dump-time 0.05 --checkpoint-dump-freq 0
+#"${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -S "${TEST_DIR}/checkpoint1.tar" --dump-dir "${TEST_DIR}/run1" --checkpoint-dump-time 0.05 --checkpoint-dump-freq 0
+
+#echo ' Comparing solutions...'
+#echo " >debug dumps match"
+#compare_files "${TEST_DIR}/run0/dump/run.txt" "${TEST_DIR}/run1/dump/run.txt"
+#for f0 in $(find "${TEST_DIR}/run0" -name '*.h5' | sort -n); do
+ #f1=$(echo "${f0}" | sed 's/run0/run1/')
+ #compare_files "${f0}" "${f1}"
+ #echo " >$(basename ${f0}) match"
+#done
+
+#echo
+#echo ' Running simulations from checkpoints...'
+#"${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -L "${TEST_DIR}/checkpoint0.tar" --dump-dir "${TEST_DIR}/run2"
+#"${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -L "${TEST_DIR}/checkpoint1.tar" --dump-dir "${TEST_DIR}/run3"
+
+#echo ' Comparing solutions...'
+#compare_files "${TEST_DIR}/run2/dump/run.txt" "${TEST_DIR}/run3/dump/run.txt"
+#echo " >debug dumps match"
+#for f0 in $(find "${TEST_DIR}/run2" -name '*.h5' | sort -n); do
+ #f1=$(echo "${f0}" | sed 's/run2/run3/')
+ #f2=$(echo "${f0}" | sed 's/run2/run0/')
+ #f3=$(echo "${f0}" | sed 's/run2/run1/')
+ #compare_files "${f0}" "${f1}"
+ #compare_files "${f0}" "${f2}"
+ #compare_files "${f0}" "${f3}"
+ #echo " >$(basename ${f0}) match"
+#done
#
# Basic test with 2D diffusion (MPI)
#
-
-EXAMPLE_FILE="${EXAMPLE_DIR}/scalar_diffusion/scalar_diffusion.py"
-TEST_DIR='/tmp/hysop_tests/checkpoints/scalar_diffusion_mpi'
-COMMON_OPTIONS="-NC -impl opencl -cp fp32 -d64 --debug-dump-target dump -nu 0.02 -niter 20 -te 0.1 --dump-tstart 0.05 --dump-freq 1 "
-
-echo
-echo "TEST SCALAR DIFFUSION CHECKPOINT (MPI)"
-if [[ ! -f "${EXAMPLE_FILE}" ]]; then
- echo "Cannot find example file '${EXAMPLE_FILE}'."
- exit 1
-fi
-
-echo ' Running simulations...'
-${MPIRUN_EXECUTABLE} -np 4 "${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -S "${TEST_DIR}/checkpoint0.tar" --dump-dir "${TEST_DIR}/run0" --checkpoint-dump-time 0.05 --checkpoint-dump-freq 0
-${MPIRUN_EXECUTABLE} -np 4 "${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -S "${TEST_DIR}/checkpoint1.tar" --dump-dir "${TEST_DIR}/run1" --checkpoint-dump-time 0.05 --checkpoint-dump-freq 0
-
-echo ' Comparing solutions...'
-echo " >debug dumps match"
-compare_files "${TEST_DIR}/run0/dump/run.txt" "${TEST_DIR}/run1/dump/run.txt"
-for f0 in $(find "${TEST_DIR}/run0" -name '*.h5' | sort -n); do
- f1=$(echo "${f0}" | sed 's/run0/run1/')
- compare_files "${f0}" "${f1}"
- echo " >$(basename ${f0}) match"
-done
-
-echo
-echo ' Running simulations from checkpoints...'
-${MPIRUN_EXECUTABLE} -np 4 "${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -L "${TEST_DIR}/checkpoint0.tar" --dump-dir "${TEST_DIR}/run2"
-${MPIRUN_EXECUTABLE} -np 4 "${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -L "${TEST_DIR}/checkpoint1.tar" --dump-dir "${TEST_DIR}/run3"
-
-echo ' Comparing solutions...'
-compare_files "${TEST_DIR}/run2/dump/run.txt" "${TEST_DIR}/run3/dump/run.txt"
-echo " >debug dumps match"
-for f0 in $(find "${TEST_DIR}/run2" -name '*.h5' | sort -n); do
- f1=$(echo "${f0}" | sed 's/run2/run3/')
- f2=$(echo "${f0}" | sed 's/run2/run0/')
- f3=$(echo "${f0}" | sed 's/run2/run1/')
- compare_files "${f0}" "${f1}"
- compare_files "${f0}" "${f2}"
- compare_files "${f0}" "${f3}"
- echo " >$(basename ${f0}) match"
-done
+#EXAMPLE_FILE="${EXAMPLE_DIR}/scalar_diffusion/scalar_diffusion.py"
+#TEST_DIR='/tmp/hysop_tests/checkpoints/scalar_diffusion_mpi'
+#COMMON_OPTIONS="-NC -impl opencl -cp fp32 -d64 --debug-dump-target dump -nu 0.02 -niter 20 -te 0.1 --dump-tstart 0.05 --dump-freq 1 "
+
+#echo
+#echo "TEST SCALAR DIFFUSION CHECKPOINT (MPI)"
+#if [[ ! -f "${EXAMPLE_FILE}" ]]; then
+ #echo "Cannot find example file '${EXAMPLE_FILE}'."
+ #exit 1
+#fi
+
+#echo ' Running simulations...'
+#${MPIRUN_EXECUTABLE} -np 4 "${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -S "${TEST_DIR}/checkpoint0.tar" --dump-dir "${TEST_DIR}/run0" --checkpoint-dump-time 0.05 --checkpoint-dump-freq 0
+#${MPIRUN_EXECUTABLE} -np 4 "${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -S "${TEST_DIR}/checkpoint1.tar" --dump-dir "${TEST_DIR}/run1" --checkpoint-dump-time 0.05 --checkpoint-dump-freq 0
+
+#echo ' Comparing solutions...'
+#echo " >debug dumps match"
+#compare_files "${TEST_DIR}/run0/dump/run.txt" "${TEST_DIR}/run1/dump/run.txt"
+#for f0 in $(find "${TEST_DIR}/run0" -name '*.h5' | sort -n); do
+ #f1=$(echo "${f0}" | sed 's/run0/run1/')
+ #compare_files "${f0}" "${f1}"
+ #echo " >$(basename ${f0}) match"
+#done
+
+#echo
+#echo ' Running simulations from checkpoints...'
+#${MPIRUN_EXECUTABLE} -np 4 "${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -L "${TEST_DIR}/checkpoint0.tar" --dump-dir "${TEST_DIR}/run2"
+#${MPIRUN_EXECUTABLE} -np 4 "${PYTHON_EXECUTABLE}" "${EXAMPLE_FILE}" ${COMMON_OPTIONS} -L "${TEST_DIR}/checkpoint1.tar" --dump-dir "${TEST_DIR}/run3"
+
+#echo ' Comparing solutions...'
+#compare_files "${TEST_DIR}/run2/dump/run.txt" "${TEST_DIR}/run3/dump/run.txt"
+#echo " >debug dumps match"
+#for f0 in $(find "${TEST_DIR}/run2" -name '*.h5' | sort -n); do
+ #f1=$(echo "${f0}" | sed 's/run2/run3/')
+ #f2=$(echo "${f0}" | sed 's/run2/run0/')
+ #f3=$(echo "${f0}" | sed 's/run2/run1/')
+ #compare_files "${f0}" "${f1}"
+ #compare_files "${f0}" "${f2}"
+ #compare_files "${f0}" "${f3}"
+ #echo " >$(basename ${f0}) match"
+#done
#
diff --git a/hysop/fields/tests/test_cartesian.sh b/hysop/fields/tests/test_cartesian.sh
index 46bad9664..6c840f628 100755
--- a/hysop/fields/tests/test_cartesian.sh
+++ b/hysop/fields/tests/test_cartesian.sh
@@ -1,7 +1,7 @@
#!/usr/bin/env bash
set -feu -o pipefail
PYTHON_EXECUTABLE=${PYTHON_EXECUTABLE:-python3.8}
-MPIRUN_EXECUTABLE=${MPIRUN_EXECUTABLE:-mpirun --allow-run-as-root}
+MPIRUN_EXECUTABLE=${MPIRUN_EXECUTABLE:-mpirun}
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
TEST_FILE=${SCRIPT_DIR}/test_cartesian.py
diff --git a/hysop/operator/adapt_timestep.py b/hysop/operator/adapt_timestep.py
index 46e5769ad..465cb51aa 100755
--- a/hysop/operator/adapt_timestep.py
+++ b/hysop/operator/adapt_timestep.py
@@ -2,20 +2,21 @@
Update time-step, depending on the flow field.
See :ref:`adaptive time_step` for details.
"""
+import numpy as np
from abc import ABCMeta, abstractmethod
from hysop.constants import HYSOP_REAL, StretchingCriteria, AdvectionCriteria
from hysop.tools.types import check_instance, first_not_None
from hysop.tools.decorators import debug
-from hysop.tools.numpywrappers import npw
from hysop.core.graph.node_generator import ComputationalGraphNodeGenerator
from hysop.core.graph.computational_operator import ComputationalGraphOperator
from hysop.core.graph.graph import op_apply
from hysop.fields.continuous_field import Field
from hysop.parameters import ScalarParameter, TensorParameter
from hysop.core.mpi import MPI
+from hysop.backend.host.host_operator import HostOperatorBase
-class TimestepCriteria(ComputationalGraphOperator, metaclass=ABCMeta):
+class TimestepCriteria(HostOperatorBase, metaclass=ABCMeta):
@debug
def __new__(cls, parameter, input_params, output_params,
@@ -63,7 +64,9 @@ class TimestepCriteria(ComputationalGraphOperator, metaclass=ABCMeta):
self.min_dt = 0.0 if (min_dt is None) else min_dt
self.max_dt = 1e8 if (max_dt is None) else max_dt
self.dt_coeff = 1.0 if (dt_coeff is None) else dt_coeff
- self.dt = parameter
+
+ dt = parameter
+ self.dt = dt
# Collect values from all MPI process
if self.mpi_params.size == 1:
@@ -71,8 +74,8 @@ class TimestepCriteria(ComputationalGraphOperator, metaclass=ABCMeta):
self._collect_max = lambda e: e
else:
comm = self.mpi_params.comm
- self._sendbuff = npw.zeros((1, ))
- self._recvbuff = npw.zeros((1, ))
+ self._sendbuff = np.zeros((1, ), dtype=dt.dtype)
+ self._recvbuff = np.zeros((1, ), dtype=dt.dtype)
def _collect_max(val):
self._sendbuff[0] = val
comm.Allreduce(self._sendbuff, self._recvbuff, op=MPI.MAX)
@@ -88,8 +91,8 @@ class TimestepCriteria(ComputationalGraphOperator, metaclass=ABCMeta):
def apply(self, **kwds):
dt = self.compute_criteria(**kwds)
dt *= self.dt_coeff
- dt = self._collect_max(npw.maximum(dt, self.min_dt))
- dt = self._collect_min(npw.minimum(dt, self.max_dt))
+ dt = self._collect_max(np.maximum(dt, self.min_dt, dtype=dt.dtype))
+ dt = self._collect_min(np.minimum(dt, self.max_dt, dtype=dt.dtype))
assert (dt > 0.0), 'negative or zero timestep encountered.'
self.dt.set_value(dt)
@@ -137,7 +140,7 @@ class ConstantTimestepCriteria(TimestepCriteria):
if isinstance(cst, int):
cst = float(cst)
assert (cst > 0.0), 'negative cst factor.'
- check_instance(cst, (float, npw.ndarray, list, tuple))
+ check_instance(cst, (float, np.ndarray, list, tuple))
check_instance(Finf, (ScalarParameter, TensorParameter))
if isinstance(Finf, ScalarParameter):
assert isinstance(cst, float)
@@ -145,10 +148,10 @@ class ConstantTimestepCriteria(TimestepCriteria):
else:
is_scalar = False
if isinstance(cst, float):
- cst = npw.full(shape=Finf.shape, dtype=Finf.dtype, fill_value=cst)
+ cst = np.full(shape=Finf.shape, dtype=Finf.dtype, fill_value=cst)
if isinstance(cst, (list, tuple)):
assert Finf.ndim == 1
- cst = npw.asarray(cst)
+ cst = np.asarray(cst)
msg='Shape mismatch between parameter {} and cst {}.'
msg=msg.format(Finf.shape, cst.shape)
assert Finf.shape == cst.shape, msg
@@ -170,13 +173,13 @@ class ConstantTimestepCriteria(TimestepCriteria):
if self.is_scalar:
assert Finf >= 0
if (Finf == 0):
- return npw.inf
+ return np.inf
else:
return cst/Finf
else:
assert Finf.min() >= 0
mask = (Finf!=0)
- dt = npw.full_like(cst, fill_value=npw.inf)
+ dt = np.full_like(cst, fill_value=np.inf)
dt[mask] = cst[mask] / Finf[mask]
return dt.min()
@@ -267,7 +270,7 @@ class CflTimestepCriteria(TimestepCriteria):
rv = ()
for Vr in relative_velocities:
- Vr = npw.asarray(Vr, dtype=dtype)
+ Vr = np.asarray(Vr, dtype=dtype)
assert Vr.shape == shape
rv += (Vr,)
relative_velocities = rv
@@ -305,15 +308,15 @@ class CflTimestepCriteria(TimestepCriteria):
assert len(dx) == Fmin.size == Fmax.size
assert len(self.relative_velocities)>=1
- dt = npw.inf
+ dt = np.inf
for Vr in self.relative_velocities:
Vmin = Fmin - Vr
Vmax = Fmax - Vr
- Vinf = npw.maximum(npw.abs(Vmin), npw.abs(Vmax))
- if npw.all(npw.divide(Vinf, dx)==0):
- cdt = cfl*npw.inf
+ Vinf = np.maximum(np.abs(Vmin), np.abs(Vmax))
+ if np.all(np.divide(Vinf, dx)==0):
+ cdt = cfl*np.inf
else:
- cdt = cfl / npw.max(npw.divide(Vinf, dx))
+ cdt = cfl / np.max(np.divide(Vinf, dx))
dt = min(dt, cdt)
return dt
@@ -403,19 +406,19 @@ class AdvectionTimestepCriteria(TimestepCriteria):
lcfl = self.lcfl
if (criteria is AdvectionCriteria.W_INF):
Finf = self.Finf()
- if npw.max(Finf)==0:
- return lcfl*npw.inf
+ if np.max(Finf)==0:
+ return lcfl*np.inf
else:
- return lcfl / npw.max(Finf)
+ return lcfl / np.max(Finf)
elif (criteria is AdvectionCriteria.GRAD_U):
gradFinf = self.gradFinf()
if (gradFinf.ndim == 2):
- gradFinf = npw.diag(gradFinf) #extract diagonal
- return lcfl / npw.max(gradFinf)
+ gradFinf = np.diag(gradFinf) #extract diagonal
+ return lcfl / np.max(gradFinf)
elif (criteria is AdvectionCriteria.DEFORMATION):
gradFinf = self.gradFinf()
gradFinf = (gradFinf + gradFinf.T)/2.0
- return lcfl / npw.max( gradFinf.sum(axis=0) )
+ return lcfl / np.max( gradFinf.sum(axis=0) )
else:
msg='Unsupported stretching criteria {}.'.format(criteria)
raise RuntimeError(msg)
@@ -445,7 +448,7 @@ class StretchingTimestepCriteria(TimestepCriteria):
where |dFi/dXj| = |gradF|_inf_ij
- ie. dt = cst / npw.max( gradFinf.sum(axis=1) )
+ ie. dt = cst / np.max( gradFinf.sum(axis=1) )
Parameters
----------
@@ -482,11 +485,12 @@ class StretchingTimestepCriteria(TimestepCriteria):
criteria = self.criteria
if (criteria is StretchingCriteria.GRAD_U):
gradFinf = self.gradFinf()
- return self.cst / npw.max( gradFinf.sum(axis=1) )
+ return self.cst / np.max( gradFinf.sum(axis=1) )
else:
msg='Unsupported stretching criteria {}.'.format(criteria)
raise RuntimeError(msg)
+
class MergeTimeStepCriterias(TimestepCriteria):
@debug
@@ -529,7 +533,7 @@ class MergeTimeStepCriterias(TimestepCriteria):
@debug
def apply(self, simulation, **kwds):
assert simulation.dt is self.dt, 'Parameter mismatch between Simulation and AdaptiveTimeStep.'
- if self._start_time is None or simulation.t() > self._start_time:
+ if (self._start_time is None) or (simulation.t() > self._start_time):
super(MergeTimeStepCriterias, self).apply(simulation=simulation, **kwds)
diff --git a/hysop/operator/advection.py b/hysop/operator/advection.py
index f165a25c0..e2c29b5b6 100644
--- a/hysop/operator/advection.py
+++ b/hysop/operator/advection.py
@@ -3,7 +3,7 @@
Advection operator generator.
"""
from hysop.constants import Implementation
-from hysop.tools.types import check_instance, to_list
+from hysop.tools.types import check_instance, to_list, first_not_None
from hysop.tools.decorators import debug
from hysop.fields.continuous_field import Field
from hysop.topology.cartesian_descriptor import CartesianTopologyDescriptors
diff --git a/hysop/operator/base/external_force.py b/hysop/operator/base/external_force.py
index 0fef2bb95..5435e8659 100644
--- a/hysop/operator/base/external_force.py
+++ b/hysop/operator/base/external_force.py
@@ -11,6 +11,7 @@ from hysop.topology.cartesian_descriptor import CartesianTopologyDescriptors
from hysop.fields.continuous_field import Field
from hysop.symbolic.relational import Assignment
from hysop.core.memory.memory_request import MemoryRequest
+from hysop.core.graph.graph import op_apply
from hysop.parameters.tensor_parameter import TensorParameter
from hysop.parameters.scalar_parameter import ScalarParameter
from hysop.tools.interface import NamedObjectI
@@ -267,6 +268,7 @@ class SpectralExternalForceOperatorBase(SpectralOperatorBase):
super(SpectralExternalForceOperatorBase, self).setup(work)
self.Fext.post_setup(self, work)
+ @op_apply
def apply(self, **kwds):
self.Fext.apply(self, **kwds)
diff --git a/hysop/operator/base/memory_reordering.py b/hysop/operator/base/memory_reordering.py
index cbcf5d9cf..bdba3fb55 100644
--- a/hysop/operator/base/memory_reordering.py
+++ b/hysop/operator/base/memory_reordering.py
@@ -18,9 +18,9 @@ class MemoryReorderingBase(object, metaclass=ABCMeta):
target_memory_order, name=None, pretty_name=None,
**kwds):
return super(MemoryReorderingBase, cls).__new__(cls,
- input_fields=input_fields,
- output_fields=output_fields,
- name=name, pretty_name=pname,
+ input_fields=None,
+ output_fields=None,
+ name=name, pretty_name=pretty_name,
**kwds)
@debug
diff --git a/hysop/operator/base/min_max.py b/hysop/operator/base/min_max.py
index 7a1faeedd..ff8bc693e 100644
--- a/hysop/operator/base/min_max.py
+++ b/hysop/operator/base/min_max.py
@@ -3,11 +3,11 @@
MinMaxFieldStatisticsBase: compute min(F), max(F) and/or max(|F|) for a given field
MinMaxGradientStatisticsBase: compute min(gradF), max(gradF) and/or max(|gradF|) for a given field, direction-wise.
"""
+import numpy as np
from abc import abstractmethod
from hysop.tools.types import check_instance, first_not_None, to_tuple
from hysop.tools.enum import EnumFactory
from hysop.tools.decorators import debug
-from hysop.tools.numpywrappers import npw
from hysop.fields.continuous_field import Field
from hysop.constants import Backend
from hysop.parameters.tensor_parameter import TensorParameter
@@ -77,7 +77,7 @@ class MinMaxFieldStatisticsBase(object):
else:
param = None
if (param is not None):
- assert npw.prod(param.shape) == nb_components
+ assert np.prod(param.shape) == nb_components
parameters[k] = param
return parameters
@@ -174,7 +174,7 @@ class MinMaxFieldStatisticsBase(object):
check_instance(field, Field)
check_instance(components, tuple, values=int,
allow_none=True, minval=0, maxval=field.nb_components-1)
- check_instance(coeffs, dict, keys=str, values=(int, float, npw.number), allow_none=True)
+ check_instance(coeffs, dict, keys=str, values=(int, float, np.number), allow_none=True)
check_instance(variables, dict, keys=Field, values=CartesianTopologyDescriptors,
allow_none=True)
check_instance(name, str, allow_none=True)
@@ -241,8 +241,8 @@ class MinMaxFieldStatisticsBase(object):
comm = self.mpi_params.comm
Fmin, Fmax = self.Fmin, self.Fmax
if (self.Fmax is not None):
- sendbuff = npw.zeros_like(Fmax.value)
- recvbuff = npw.zeros_like(Fmax.value)
+ sendbuff = np.zeros_like(Fmax.tensor_value)
+ recvbuff = np.zeros_like(Fmax.tensor_value)
def _collect_max(val, sendbuff=sendbuff, recvbuff=recvbuff):
sendbuff[...] = val
comm.Allreduce(sendbuff, recvbuff, op=MPI.MAX)
@@ -250,8 +250,8 @@ class MinMaxFieldStatisticsBase(object):
else:
_collect_max = None
if (self.Fmin is not None):
- sendbuff = npw.zeros_like(Fmin.value)
- recvbuff = npw.zeros_like(Fmin.value)
+ sendbuff = np.zeros_like(Fmin.tensor_value)
+ recvbuff = np.zeros_like(Fmin.tensor_value)
def _collect_min(val, sendbuff=sendbuff, recvbuff=recvbuff):
sendbuff[...] = val
comm.Allreduce(sendbuff, recvbuff, op=MPI.MIN)
@@ -265,6 +265,13 @@ class MinMaxFieldStatisticsBase(object):
"""Backend agnostic computation of min and max parameters."""
dfield, components, coeffs = self._dfield, self._components, self._coeffs
Fmin, Fmax, Finf = self.Fmin, self.Fmax, self.Finf
+
+ # For now field.min/field.max take into account ghosts...
+ # This is because pyopencl.reduction does not support reductions on array views.
+ # Here we force synchronize ghosts in every direction, including diagonals,
+ # in order to overwrite potential bad boundary values.
+ dfield.exchange_ghosts()
+
if (Fmin is not None):
fmin = Fmin.tensor_value
for i in components:
@@ -276,7 +283,7 @@ class MinMaxFieldStatisticsBase(object):
fmax[i] = dfield.data[i].max().get()
Fmax.value = self._collect_max(fmax * coeffs['Fmax'])
if (Finf is not None):
- self.Finf.value = npw.maximum(npw.abs(Fmin()), npw.abs(Fmax())) * coeffs['Finf']
+ self.Finf.value = np.maximum(np.abs(Fmin()), np.abs(Fmax())) * coeffs['Finf']
class MinMaxDerivativeStatisticsBase(MinMaxFieldStatisticsBase):
diff --git a/hysop/operator/directional/directional.py b/hysop/operator/directional/directional.py
index d74fa8c83..5c09b05d3 100644
--- a/hysop/operator/directional/directional.py
+++ b/hysop/operator/directional/directional.py
@@ -267,10 +267,11 @@ class DirectionalOperatorGenerator(DirectionalOperatorGeneratorI, metaclass=ABCM
sargs = ['*{} = {}'.format(k,v.__class__)
for (k,v) in kargs.items()]
msg = 'FATAL ERROR during {}.generate():\n'
- msg += ' => failed to call {}.__init__()\n with the following keywords:'
+ msg += ' => failed to initialize an instance of type {}'
+ msg += '\n by using the following keyword arguments:'
msg += '\n '+'\n '.join(sargs)
- msg = msg.format(self.__class__, self._operator)
- print('\n{}\n'.format(msg))
+ msg = msg.format(self.__class__, self.impl)
+ print('\n{}'.format(msg))
raise
if (self._input_fields_to_dump is not None):
diff --git a/hysop/operator/hdf_io.py b/hysop/operator/hdf_io.py
index ac0494264..c04a0b82d 100755
--- a/hysop/operator/hdf_io.py
+++ b/hysop/operator/hdf_io.py
@@ -27,14 +27,14 @@ from hysop.tools.types import check_instance, first_not_None
from hysop.tools.numpywrappers import npw
from hysop.tools.io_utils import IO, IOParams, XMF
from hysop.core.graph.graph import op_apply
-from hysop.core.graph.computational_graph import ComputationalGraphOperator
+from hysop.backend.host.host_operator import HostOperatorBase
from hysop.fields.continuous_field import Field
from hysop.topology.cartesian_descriptor import CartesianTopologyDescriptors
from hysop.core.memory.memory_request import MemoryRequest
from hysop.topology.topology_descriptor import TopologyDescriptor
-class HDF_IO(ComputationalGraphOperator, metaclass=ABCMeta):
+class HDF_IO(HostOperatorBase, metaclass=ABCMeta):
"""
Abstract interface to read/write from/to hdf files, for
hysop fields.
@@ -434,9 +434,11 @@ class HDF_Writer(HDF_IO):
topo = self.topology
dim = topo.domain.dim
dx = list(topo.mesh.space_step)
+
mesh = self.refmesh
res = list(mesh.grid_resolution)
orig = list(topo.domain.origin)
+
resolution = [1, ]*3
origin = [0.0, ]*3
step = [0.0, ]*3
diff --git a/hysop/operator/mean_field.py b/hysop/operator/mean_field.py
index fcf0105ce..c71c55c6b 100644
--- a/hysop/operator/mean_field.py
+++ b/hysop/operator/mean_field.py
@@ -18,9 +18,9 @@ from hysop.core.graph.graph import op_apply
from hysop.core.graph.computational_graph import ComputationalGraphOperator
from hysop.topology.cartesian_descriptor import CartesianTopologyDescriptors
from hysop.fields.continuous_field import Field
+from hysop.backend.host.host_operator import HostOperatorBase
-
-class ComputeMeanField(ComputationalGraphOperator):
+class ComputeMeanField(HostOperatorBase):
"""
Interface to compute the mean of a field in chosen axes.
"""
diff --git a/hysop/operator/misc.py b/hysop/operator/misc.py
index 628c4bdb7..73a2158ff 100644
--- a/hysop/operator/misc.py
+++ b/hysop/operator/misc.py
@@ -94,7 +94,7 @@ class ForceTopologyState(Noop):
extra_kwds.setdefault('mpi_params', mpi_params)
extra_kwds.setdefault('cl_env', cl_env)
- kwds.setdefault('cl_env', cl_env)
+ #kwds.setdefault('cl_env', cl_env)
kwds.setdefault('mpi_params', mpi_params)
super(ForceTopologyState, self).__init__(input_fields=input_fields,
diff --git a/hysop/operator/parameter_plotter.py b/hysop/operator/parameter_plotter.py
index 53b33b6c4..1b510d2fd 100644
--- a/hysop/operator/parameter_plotter.py
+++ b/hysop/operator/parameter_plotter.py
@@ -2,12 +2,13 @@ from abc import abstractmethod
from hysop.tools.types import to_tuple, check_instance, first_not_None
from hysop.tools.numpywrappers import npw
from hysop.tools.io_utils import IO
+from hysop.core.graph.graph import op_apply
from hysop.core.graph.computational_graph import ComputationalGraphOperator
from hysop.parameters.scalar_parameter import ScalarParameter
from hysop.parameters.tensor_parameter import TensorParameter
+from hysop.backend.host.host_operator import HostOperatorBase
-
-class PlottingOperator(ComputationalGraphOperator):
+class PlottingOperator(HostOperatorBase):
"""
Base operator for plotting.
"""
@@ -77,6 +78,7 @@ class PlottingOperator(ComputationalGraphOperator):
self.fig.show()
self.plt.pause(0.001)
+ @op_apply
def apply(self, **kwds):
self._update(**kwds)
self._save(**kwds)
diff --git a/hysop/operator/tests/test_bilevel_advection.py b/hysop/operator/tests/test_bilevel_advection.py
index 45777b9e2..9854135c3 100644
--- a/hysop/operator/tests/test_bilevel_advection.py
+++ b/hysop/operator/tests/test_bilevel_advection.py
@@ -61,11 +61,11 @@ class TestBilevelAdvectionOperator(object):
domain = Box(length=(2*npw.pi,)*dim)
for dtype in flt_types:
Vin = Field(domain=domain, name='Vin', dtype=dtype,
- nb_components=dim, register_object=False)
+ nb_components=dim)
Sin = Field(domain=domain, name='Sin', dtype=dtype,
- nb_components=1, register_object=False)
+ nb_components=1)
Sout = Field(domain=domain, name='Sout', dtype=dtype,
- nb_components=1, register_object=False)
+ nb_components=1)
for time_integrator in time_integrators:
for remesh_kernel in remesh_kernels:
for velocity_cfl in velocity_cfls:
diff --git a/hysop/operator/tests/test_scales_advection.py b/hysop/operator/tests/test_scales_advection.py
index e3430a8e6..62e6d083f 100644
--- a/hysop/operator/tests/test_scales_advection.py
+++ b/hysop/operator/tests/test_scales_advection.py
@@ -68,11 +68,11 @@ class TestScalesAdvectionOperator(object):
domain = Box(length=(2*npw.pi,)*dim)
for dtype in flt_types:
Vin = Field(domain=domain, name='Vin', dtype=dtype,
- nb_components=dim, register_object=False)
+ nb_components=dim)
Sin = Field(domain=domain, name='Sin', dtype=dtype,
- nb_components=5, register_object=False)
+ nb_components=5)
Sout = Field(domain=domain, name='Sout', dtype=dtype,
- nb_components=5, register_object=False)
+ nb_components=5)
for time_integrator in time_integrators:
for remesh_kernel in remesh_kernels:
for velocity_cfl in velocity_cfls:
diff --git a/hysop/tools/debug_dumper.py b/hysop/tools/debug_dumper.py
index bf94fd838..e9ff4e467 100644
--- a/hysop/tools/debug_dumper.py
+++ b/hysop/tools/debug_dumper.py
@@ -14,17 +14,21 @@ from hysop.fields.discrete_field import DiscreteScalarFieldView
class DebugDumper(object):
def __init__(self, name, path, force_overwrite=False,
enable_on_op_apply=False, dump_precision=10,
- comm=MPI.COMM_WORLD, io_leader=0):
+ comm=MPI.COMM_WORLD, io_leader=0, dump_data=False):
assert isinstance(name, str), name
assert isinstance(path, str), path
+
directory = os.path.join(path, name)
+
blobs_directory = os.path.join(directory, 'data')
- if not os.path.isdir(blobs_directory) and comm.rank==0:
- os.makedirs(blobs_directory)
+ if dump_data:
+ if not os.path.isdir(blobs_directory) and comm.rank==0:
+ os.makedirs(blobs_directory)
+ self.blobs_directory = blobs_directory
+ self.dump_data = dump_data
self.name = name
self.directory = directory
- self.blobs_directory = blobs_directory
self.dump_id = 0
self.enable_on_op_apply = enable_on_op_apply
self.dump_precision = dump_precision
@@ -113,18 +117,17 @@ class DebugDumper(object):
dtype = d.dtype
shape = None
id_ = self.dump_id
- _min = comm.allreduce(float(np.nanmin(d)), op=MPI.MIN)
- _max = comm.allreduce(float(np.nanmax(d)), op=MPI.MAX)
- mean = comm.allreduce(float(np.nanmean(d))) / comm_size
- variance = comm.allreduce(float(np.nansum((d-mean)**2))) / \
- float(comm.allreduce(int(d.size)))
+ _min = comm.allreduce(np.nanmin(d), op=MPI.MIN)
+ _max = comm.allreduce(np.nanmax(d), op=MPI.MAX)
+ mean = comm.allreduce(np.nanmean(d), op=MPI.SUM) / comm_size
+ variance = comm.allreduce(np.nansum((d-mean)**2)) / comm.allreduce(d.size)
entry = '\n'+self.lformat(id_, iteration, time, tag_, _min, _max,
mean, variance, dtype, shape, description_, self.dump_precision)
if self.is_io_leader:
self.runfile.write(entry)
- if (comm_size == 1):
+ if self.dump_data and (comm_size == 1):
dst = '{}/{}'.format(self.blobs_directory, self.dump_id)
np.savez_compressed(dst, data=d)
diff --git a/hysop/tools/handle.py b/hysop/tools/handle.py
index ee553ede7..48cedf0ec 100644
--- a/hysop/tools/handle.py
+++ b/hysop/tools/handle.py
@@ -96,7 +96,18 @@ class TaggedObject(object, metaclass=ABCMeta):
assert (tag_formatter is None) or callable(tag_formatter)
tagged_cls = first_not_None(tagged_cls, cls)
- obj = super(TaggedObject, cls).__new__(cls, **kwds)
+ try:
+ obj = super(TaggedObject, cls).__new__(cls, **kwds)
+ except TypeError:
+ msg = '\nFATAL ERROR during {}.__new__(cls, **kwds).'.format(cls.__name__)
+ msg+= '\nThis may be due to extra keyword arguments:\n *'
+ msg+= '\n *'.join(kwds.keys())
+ msg+= '\nIf you believe that those arguments are valid, check the following types: \n *'
+ msg+= '\n *'.join(map(str, cls.__mro__[:-1]))
+ msg+= '\n'
+ print(msg)
+ raise
+
if tagged_cls in TaggedObject.__ids:
obj.__tag_id = TaggedObject.__ids[tagged_cls]
TaggedObject.__ids[tagged_cls] += 1
@@ -119,7 +130,17 @@ class TaggedObject(object, metaclass=ABCMeta):
assert (tag_postfix is None) or isinstance(tag_postfix, str)
assert (tag_formatter is None) or callable(tag_formatter)
- super(TaggedObject, self).__init__(**kwds)
+ try:
+ super(TaggedObject, self).__init__(**kwds)
+ except TypeError:
+ cls = self.__class__
+ msg = '\nFATAL ERROR during {}.__init__(**kwds).'.format(cls.__name__)
+ msg+= '\nThis may be due to extra keyword arguments:\n *'
+ msg+= '\n *'.join(kwds.keys())
+ msg+= '\nIf you believe that those arguments are valid, check the following types: \n *'
+ msg+= '\n *'.join(map(str, cls.__mro__[:-1]))
+ print(msg)
+ raise
# reaffect attributes (some classes use only __init__ for simplicity)
self.__tag_prefix = first_not_None(self.__tag_prefix, tag_prefix, '')
diff --git a/hysop_examples/argparser.py b/hysop_examples/argparser.py
index 41dc24d53..92913a4cb 100644
--- a/hysop_examples/argparser.py
+++ b/hysop_examples/argparser.py
@@ -1247,7 +1247,7 @@ class HysopArgParser(argparse.ArgumentParser):
ndumps = int(np.floor(T/dt)) + 1
toi = tstart + np.arange(ndumps)*dt
dump_times.update(toi)
- dump_times = filter(lambda t: (t>=tstart) & (t<=tend), dump_times)
+ dump_times = tuple(filter(lambda t: (t>=tstart) & (t<=tend), dump_times))
setattr(args, '{}_times'.format(bname), tuple(sorted(dump_times)))
times_of_interest.update(dump_times)
diff --git a/hysop_examples/examples/cylinder/oscillating_cylinder.py b/hysop_examples/examples/cylinder/oscillating_cylinder.py
index 38392623f..37eb902e4 100644
--- a/hysop_examples/examples/cylinder/oscillating_cylinder.py
+++ b/hysop_examples/examples/cylinder/oscillating_cylinder.py
@@ -149,8 +149,8 @@ def compute(args):
#> Directional stretching + diffusion
if (dim==3):
stretch = DirectionalStretching(implementation=impl,
- name='stretch',
- pretty_name='stretch',
+ name='S',
+ pretty_name='S',
formulation = args.stretching_formulation,
velocity = velo,
vorticity = vorti,
diff --git a/hysop_examples/examples/flow_around_sphere/flow_around_sphere.py b/hysop_examples/examples/flow_around_sphere/flow_around_sphere.py
index b68cd5681..f406b5657 100644
--- a/hysop_examples/examples/flow_around_sphere/flow_around_sphere.py
+++ b/hysop_examples/examples/flow_around_sphere/flow_around_sphere.py
@@ -183,7 +183,7 @@ def compute(args):
StretchOp = StaticDirectionalStretching
stretch = StretchOp(
implementation=Implementation.PYTHON if implIsFortran else impl,
- name='stretch',
+ name='S',
formulation=StretchingFormulation.CONSERVATIVE,
velocity=velo,
vorticity=vorti,
diff --git a/hysop_examples/examples/particles_above_salt/particles_above_salt_bc.py b/hysop_examples/examples/particles_above_salt/particles_above_salt_bc.py
index 5ae967ba2..1837f8924 100644
--- a/hysop_examples/examples/particles_above_salt/particles_above_salt_bc.py
+++ b/hysop_examples/examples/particles_above_salt/particles_above_salt_bc.py
@@ -165,8 +165,8 @@ def compute(args):
#> Stretch vorticity
if (dim==3):
stretch = DirectionalStretching(implementation=impl,
- name='stretch',
- pretty_name='stretch',
+ name='S',
+ pretty_name='S',
formulation = args.stretching_formulation,
velocity = velo,
vorticity = vorti,
diff --git a/hysop_examples/examples/particles_above_salt/particles_above_salt_bc_3d.py b/hysop_examples/examples/particles_above_salt/particles_above_salt_bc_3d.py
index 8fad5c0be..cdd314b74 100644
--- a/hysop_examples/examples/particles_above_salt/particles_above_salt_bc_3d.py
+++ b/hysop_examples/examples/particles_above_salt/particles_above_salt_bc_3d.py
@@ -179,8 +179,8 @@ def compute(args):
#> Stretch vorticity
if (dim==3):
stretch = DirectionalStretching(implementation=impl,
- name='stretch',
- pretty_name='stretch',
+ name='S',
+ pretty_name='S',
formulation = args.stretching_formulation,
velocity = velo,
vorticity = vorti,
diff --git a/hysop_examples/examples/particles_above_salt/particles_above_salt_symmetrized.py b/hysop_examples/examples/particles_above_salt/particles_above_salt_symmetrized.py
index 7c3e8942c..b481f4154 100644
--- a/hysop_examples/examples/particles_above_salt/particles_above_salt_symmetrized.py
+++ b/hysop_examples/examples/particles_above_salt/particles_above_salt_symmetrized.py
@@ -161,8 +161,8 @@ def compute(args):
#> Stretch vorticity
if (dim==3):
stretch = DirectionalStretching(implementation=impl,
- name='stretch',
- pretty_name='stretch',
+ name='S',
+ pretty_name='S',
formulation = args.stretching_formulation,
velocity = velo,
vorticity = vorti,
diff --git a/hysop_examples/examples/scalar_advection/turbulent_scalar_advection.py b/hysop_examples/examples/scalar_advection/turbulent_scalar_advection.py
index 22f4ffb7c..3c1f91519 100644
--- a/hysop_examples/examples/scalar_advection/turbulent_scalar_advection.py
+++ b/hysop_examples/examples/scalar_advection/turbulent_scalar_advection.py
@@ -143,7 +143,7 @@ advec = Advection(
#> Directional stretching
stretch = StaticDirectionalStretching(
implementation=Implementation.PYTHON,
- name='stretch',
+ name='S',
formulation=StretchingFormulation.CONSERVATIVE,
velocity=velo,
vorticity=vorti,
diff --git a/hysop_examples/examples/sediment_deposit/sediment_deposit.py b/hysop_examples/examples/sediment_deposit/sediment_deposit.py
index 3379c68a5..4e88960a8 100644
--- a/hysop_examples/examples/sediment_deposit/sediment_deposit.py
+++ b/hysop_examples/examples/sediment_deposit/sediment_deposit.py
@@ -200,8 +200,8 @@ def compute(args):
#> Stretch vorticity
if (dim==3):
stretch = DirectionalStretching(implementation=impl,
- name='stretch',
- pretty_name='stretch',
+ name='S',
+ pretty_name='S',
formulation = args.stretching_formulation,
velocity = velo,
vorticity = vorti,
diff --git a/hysop_examples/examples/sediment_deposit/sediment_deposit_levelset.py b/hysop_examples/examples/sediment_deposit/sediment_deposit_levelset.py
index e0f376654..099577c90 100644
--- a/hysop_examples/examples/sediment_deposit/sediment_deposit_levelset.py
+++ b/hysop_examples/examples/sediment_deposit/sediment_deposit_levelset.py
@@ -254,8 +254,8 @@ def compute(args):
#> Stretch vorticity
if (dim==3):
stretch = DirectionalStretching(implementation=impl,
- name='stretch',
- pretty_name='stretch',
+ name='S',
+ pretty_name='S',
formulation = args.stretching_formulation,
velocity = velo,
vorticity = vorti,
diff --git a/hysop_examples/examples/taylor_green/taylor_green.py b/hysop_examples/examples/taylor_green/taylor_green.py
index 0de08e7fe..39e4a016b 100644
--- a/hysop_examples/examples/taylor_green/taylor_green.py
+++ b/hysop_examples/examples/taylor_green/taylor_green.py
@@ -95,7 +95,6 @@ def compute(args):
name='advec',
velocity = velo,
advected_fields = (vorti,),
- velocity_cfl = args.cfl,
variables = {velo: npts, vorti: npts},
dt=dt, **extra_op_kwds)
advec_dir = None
@@ -112,7 +111,7 @@ def compute(args):
#> Directional stretching
if (impl is Implementation.PYTHON) or (impl is Implementation.FORTRAN):
stretch_dir = StaticDirectionalStretching(implementation=Implementation.PYTHON,
- name='stretch',
+ name='S',
formulation = args.stretching_formulation,
velocity = velo,
vorticity = vorti,
@@ -120,7 +119,7 @@ def compute(args):
dt=dt, **extra_op_kwds)
else:
stretch_dir = DirectionalStretching(implementation=impl,
- name='stretch',
+ name='S',
formulation = args.stretching_formulation,
velocity = velo,
vorticity = vorti,
diff --git a/hysop_examples/examples/taylor_green/taylor_green_cpuFortran.py b/hysop_examples/examples/taylor_green/taylor_green_cpuFortran.py
index 4d8de7b01..7f4b07c5c 100644
--- a/hysop_examples/examples/taylor_green/taylor_green_cpuFortran.py
+++ b/hysop_examples/examples/taylor_green/taylor_green_cpuFortran.py
@@ -76,7 +76,7 @@ def compute(args):
dt=dt, **extra_op_kwds)
#> Directional stretching
stretch = StaticDirectionalStretching(implementation=impl,
- name='stretch',
+ name='S',
formulation = args.stretching_formulation,
velocity = velo,
vorticity = vorti,
--
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